2-237342081-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_004369.4(COL6A3):c.7749G>A(p.Thr2583Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000576 in 1,614,034 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004369.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.7749G>A | p.Thr2583Thr | synonymous_variant | Exon 37 of 44 | ENST00000295550.9 | NP_004360.2 | |
COL6A3 | NM_057167.4 | c.7131G>A | p.Thr2377Thr | synonymous_variant | Exon 36 of 43 | NP_476508.2 | ||
COL6A3 | NM_057166.5 | c.5928G>A | p.Thr1976Thr | synonymous_variant | Exon 34 of 41 | NP_476507.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251374Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135854
GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461816Hom.: 1 Cov.: 30 AF XY: 0.0000564 AC XY: 41AN XY: 727204
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Bethlem myopathy 1A Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at